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- PDB-7kov: Crystal structure of Azotobacter vinelandii 3-mercaptopropionic a... -

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Basic information

Entry
Database: PDB / ID: 7kov
TitleCrystal structure of Azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in complex with thiocyanate
ComponentsCysteine dioxygenase type I protein
KeywordsOXIDOREDUCTASE / non-heme iron / facial triad / thiocyanate
Function / homologyCysteine dioxygenase type I / Cysteine dioxygenase type I / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / ferrous iron binding / : / THIOCYANATE ION / Cysteine dioxygenase type I protein
Function and homology information
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsKiser, P.D.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structure of 3-mercaptopropionic acid dioxygenase with a substrate analog reveals bidentate substrate binding at the iron center.
Authors: York, N.J. / Lockart, M.M. / Sardar, S. / Khadka, N. / Shi, W. / Stenkamp, R.E. / Zhang, J. / Kiser, P.D. / Pierce, B.S.
History
DepositionNov 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Cysteine dioxygenase type I protein
A: Cysteine dioxygenase type I protein
C: Cysteine dioxygenase type I protein
D: Cysteine dioxygenase type I protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,17114
Polymers93,6454
Non-polymers52710
Water43224
1
B: Cysteine dioxygenase type I protein
C: Cysteine dioxygenase type I protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1218
Polymers46,8222
Non-polymers2996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-50 kcal/mol
Surface area17400 Å2
MethodPISA
2
A: Cysteine dioxygenase type I protein
D: Cysteine dioxygenase type I protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0506
Polymers46,8222
Non-polymers2284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-43 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.182, 102.182, 301.935
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11C-303-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14A
24C
15A
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLNGLNBA5 - 1955 - 195
21PROPROGLNGLNAB5 - 1955 - 195
12PROPROGLNGLNBA5 - 1955 - 195
22PROPROGLNGLNCC5 - 1955 - 195
13PROPROGLNGLNBA5 - 1955 - 195
23PROPROGLNGLNDD5 - 1955 - 195
14SERSERSERSERAB4 - 1964 - 196
24SERSERSERSERCC4 - 1964 - 196
15SERSERSERSERAB4 - 1964 - 196
25SERSERSERSERDD4 - 1964 - 196
16SERSERSERSERCC4 - 1964 - 196
26SERSERSERSERDD4 - 1964 - 196

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Cysteine dioxygenase type I protein


Mass: 23411.135 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C1DN94
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.05 M HEPES pH 7, 44% pentaerythritol propoxylate (5/4 PO/OH), 0.6 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 20505 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.468 / Rmerge(I) obs: 0.185 / Net I/σ(I): 12.9
Reflection shellResolution: 2.95→3.13 Å / Rmerge(I) obs: 2.883 / Num. unique obs: 3185 / CC1/2: 0.468

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XB9

6xb9


Resolution: 2.95→49.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.948 / SU B: 24.241 / SU ML: 0.395 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 1026 5 %RANDOM
Rwork0.2149 ---
obs0.2162 19476 99.78 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 183.4 Å2 / Biso mean: 97.703 Å2 / Biso min: 59.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20.89 Å20 Å2
2--1.78 Å2-0 Å2
3----5.76 Å2
Refinement stepCycle: final / Resolution: 2.95→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6124 0 18 24 6166
Biso mean--111.56 81.39 -
Num. residues----773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136304
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175747
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.6418573
X-RAY DIFFRACTIONr_angle_other_deg1.0491.57913205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6755769
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60320.495404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60715955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9351572
X-RAY DIFFRACTIONr_chiral_restr0.0370.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021570
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B60150.03
12A60150.03
21B60220.04
22C60220.04
31B60050.04
32D60050.04
41A60490.04
42C60490.04
51A60350.03
52D60350.03
61C60450.04
62D60450.04
LS refinement shellResolution: 2.951→3.028 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 73 -
Rwork0.403 1378 -
all-1451 -
obs--98.31 %

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